CDI Type II Computational Discovery of Unusual Nucleic-Acid-Based Nanostructures

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CBET-0835794HallDNA can be possibly used to construct tiny scaffolds with many potential applications including molecular medicine, electronics, sensors, computing and communications equipment, and consumer electronics. Two-dimensional nanostructures have already been devised, but further design and development has so far been limited to making incremental improvements using empirically derived guidelines. This project intends to break these barriers using advanced modeling techniques, a multidisciplinary team of modelers and experimentalists, and a cyber-driven strategy to design complex, three-dimensional objects at nanometer size scales. First, modified natural and non-natural nucleosides (the components RNA) will be devised to increase the number of molecular tools available to create these structures and to provide accessible sites for attachment of functional components. Structures will be computed for these two- and three-dimensional DNA-based building blocks, with and without modified nucleosides. Stability will then be determined for the building blocks in solution, on planar surfaces, and/or with metallic nanoparticles. Ultimately, new, hybrid extended three-dimensional architectures will be designed and built using these findings. A key to success is testing and refining the modeling approaches by comparing computed results to the team's experimental results. The education and outreach agenda includes a team mentoring program for a small group of women graduate and undergraduate students, individual outreach efforts to underrepresented groups, and training of four graduate students and four undergraduates. Cyber-enabled education is an especially interesting aspect of the project, where a website containing freely-available cyber-structure software and visuals will allow researchers to design their own DNA superstructures and will also allow community members, including grades 7-12, to learn more about DNA self-assembly.